public void ReadInMasterFile()
{
UpdateText("Reading GC Master File...");
master = new Master(gcMastTextBox.Text);
master.ReadInMaster();
UpdateText("Preparing GC Results Database...");
SQLiteIOMethods.CreateQuantDatabase(outputDirectoryTextBox.Text, out conn);
SQLiteIOMethods.AddBatchStructure(BatchDictionary, conn);
SQLiteIOMethods.AddMasterInformationToDatabase(conn, gcMastTextBox.Text);
UpdateText("Starting Quantitation...");
MasterReadInFinished();
}
public static void ProcessData(SQLiteConnection conn)
{
Dictionary <int, Batch> batchDict = GetBatchDictionary(conn);
PopulateReplicateQuantDict(batchDict, conn);
//NEW
var refBatch = GetMedianReferenceExperiment(batchDict);
foreach (var batch in batchDict.Values)
{
foreach (var rep in batch.replicates)
{
//NormalizeRepToReferenceExperiment(refBatch, rep);
NormalizeRepToRefExperimentLinear(refBatch, rep);
}
}
GetAveragedIntensityValues(batchDict);
GetBatchLessControlValues(batchDict);
SQLiteIOMethods.AddBarChartInfoToDatabase(batchDict, conn);
SQLiteIOMethods.AddBatchQuantDataToDatabase(batchDict, conn);
SQLiteIOMethods.AddBatchBatchCorrelationsToDatabase(batchDict, conn);
//OLD
//GetAveragedIntensityValues(batchDict);
//GetBatchLessControlValues(batchDict);
//GetInternalStandards(batchDict, conn);
//List<InternalStandard> standards = new List<InternalStandard>();
//foreach (var batch in batchDict.Values)
//{
// foreach (var rep in batch.replicates)
// {
// foreach (var standard in rep.internalStandards)
// {
// standards.Add(standard);
// }
// }
//}
//SQLiteIOMethods.AddInternalStandardsToDatabase(standards, conn);
//SQLiteIOMethods.AddBatchQuantDataToDatabase(batchDict, conn);
}
public void Quantify()
{
List <EISpectrum> curatedSpectra = Master.allSpectra.Where(x => x.isValid).ToList();
List <RTPeak> replicateTIC = SQLiteIOMethods.GetTicChromaFromGCFeat(ReplicateDBConnection);
ClippedMasterTicChroma = RemoveSolventFrontFromTIC(Master.chroma);
ClippedReplicateTicChroma = RemoveSolventFrontFromTIC(replicateTIC, replicateTIC.First().RT);
int completed = 0;
using (var transaction = QuantDbConnection.BeginTransaction())
{
foreach (var currentSpectrum in curatedSpectra)
{
if (!SQLiteIOMethods.IsQuantified(CurrentReplicate.replicateID, QuantDbConnection))
{
double apexTime = currentSpectrum.ApexTimeEI;
double startTime = apexTime - .15;
double stopTime = apexTime + .15;
GetValidTICSegment(startTime, stopTime);
CurrentTICStartTime = startTime;
CurrentTICStopTime = stopTime;
var ticMaster =
ClippedMasterTicChroma.Where(x => x.RT >= CurrentTICStartTime && x.RT <= CurrentTICStopTime)
.ToList();
var ticReplicate =
ClippedReplicateTicChroma.Where(x => x.RT >= CurrentTICStartTime && x.RT <= CurrentTICStopTime)
.ToList();
var ticMasterArray = GetExpandedChromatogram(ticMaster, CurrentTICStartTime, CurrentTICStopTime);
var ticReplicateArray = GetExpandedChromatogram(ticReplicate, CurrentTICStartTime,
CurrentTICStopTime);
double offset = GetAdjustedChromatogramOffset(ticMasterArray, ticReplicateArray);
DoubleRange quantRange = new DoubleRange(currentSpectrum.ApexTimeEI - offset - .15,
currentSpectrum.ApexTimeEI - offset + .15);
List <Feature> replicateRangeFeatures = SQLiteIOMethods.GetFeatures(quantRange.Minimum,
quantRange.Maximum, ReplicateDBConnection);
List <Feature> currSpecQuantFeatures = new List <Feature>();
foreach (var ion in currentSpectrum.quantIons)
{
var ppmRange = DoubleRange.FromPPM(ion.MZ, 5);
currSpecQuantFeatures.AddRange(replicateRangeFeatures.Where(x => ppmRange.Contains(x.AverageMZ)));
}
foreach (var ion in currentSpectrum.quantIons)
{
var ppmRange = DoubleRange.FromPPM(ion.MZ, 5);
Feature quantFeature = null;
double timeDifference = double.MaxValue;
foreach (var feature in currSpecQuantFeatures)
{
if (ppmRange.Contains(feature.AverageMZ))
{
var currTimeDiff = Math.Abs(feature.apexTime - currentSpectrum.ApexTimeEI - offset);
if (currTimeDiff < timeDifference)
{
timeDifference = currTimeDiff;
quantFeature = feature;
}
}
}
if (quantFeature != null)
{
if (CurrentReplicate.control != null)
{
SQLiteIOMethods.AddReplicateQuantPointToDatabase(CurrentReplicate.replicateID, CurrentReplicate.name, CurrentReplicate.batchID, CurrentReplicate.control.batchID,
currentSpectrum.FeatureGroup.groupID, offset, quantFeature, QuantDbConnection);
}
else
{
SQLiteIOMethods.AddReplicateQuantPointToDatabase(CurrentReplicate.replicateID, CurrentReplicate.name, CurrentReplicate.batchID, 0, currentSpectrum.FeatureGroup.groupID,
offset, quantFeature, QuantDbConnection);
}
}
else
{
if (CurrentReplicate.control != null)
{
SQLiteIOMethods.AddNullReplicateQuantPointToDatabase(CurrentReplicate.replicateID, CurrentReplicate.name, CurrentReplicate.batchID, CurrentReplicate.control.batchID,
currentSpectrum.FeatureGroup.groupID, offset, QuantDbConnection);
}
else
{
SQLiteIOMethods.AddNullReplicateQuantPointToDatabase(CurrentReplicate.replicateID, CurrentReplicate.name, CurrentReplicate.batchID, 0,
currentSpectrum.FeatureGroup.groupID, offset, QuantDbConnection);
}
}
}
completed++;
double percent = ((double)completed) / ((double)curatedSpectra.Count) * 200;
OnProgressUpdate(percent);
}
}
SQLiteIOMethods.SetReplicateToQuantified(CurrentReplicate.replicateID, QuantDbConnection);
transaction.Commit();
transaction.Dispose();
}
OnFinish();
}